[English] 日本語
Yorodumi
- PDB-6k4z: Single-chain Fv antibody of C6 COMPLEXED WITH 2-(4-HYDROXY-3-NITR... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6k4z
TitleSingle-chain Fv antibody of C6 COMPLEXED WITH 2-(4-HYDROXY-3-NITROPHENYL)ACETIC ACID
ComponentsscFv of C6
KeywordsIMMUNE SYSTEM / antigen binding / affinity maturation / Somatic hypermutation / conformational change
Function / homology2-(4-HYDROXY-3-NITROPHENYL)ACETIC ACID
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsNishiguchi, A. / Numoto, N. / Ito, N. / Azuma, T. / Oda, M.
CitationJournal: Mol.Immunol. / Year: 2019
Title: Three-dimensional structure of a high affinity anti-(4-hydroxy-3-nitrophenyl)acetyl antibody possessing a glycine residue at position 95 of the heavy chain.
Authors: Nishiguchi, A. / Numoto, N. / Ito, N. / Azuma, T. / Oda, M.
History
DepositionMay 27, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 18, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 2, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: scFv of C6
B: scFv of C6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,8166
Polymers52,2342
Non-polymers5824
Water9,764542
1
A: scFv of C6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,5024
Polymers26,1171
Non-polymers3853
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area10480 Å2
MethodPISA
2
B: scFv of C6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,3142
Polymers26,1171
Non-polymers1971
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area150 Å2
ΔGint-10 kcal/mol
Surface area10470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.393, 46.779, 74.581
Angle α, β, γ (deg.)88.235, 103.780, 111.984
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

-
Components

#1: Antibody scFv of C6


Mass: 26116.920 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: The fusion protein of expression tags (residues -2-0), the light chain (residues 1-108), linker GGGGSGGGGSGGGGS (residues 501-515), and the heavy chain (residues 1001-1113)
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pET-32TH / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): codon plus
#2: Chemical ChemComp-NPA / 2-(4-HYDROXY-3-NITROPHENYL)ACETIC ACID


Mass: 197.145 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H7NO5 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 542 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.37 Å3/Da / Density % sol: 48.13 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.14 M Lithium sulfate monohydrate, 0.07 M TRIS hydrochloride pH 8.5, 21% w/v Polyethylene glycol 4000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1.1 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Dec 12, 2018
RadiationMonochromator: Cryo-cooled channel-cut Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.65→50 Å / Num. obs: 52628 / % possible obs: 96.2 % / Redundancy: 3.6 % / Biso Wilson estimate: 17.07 Å2 / CC1/2: 0.998 / Rsym value: 0.073 / Net I/σ(I): 11.2
Reflection shellResolution: 1.65→1.75 Å / Redundancy: 3.5 % / Num. unique obs: 8339 / CC1/2: 0.716 / Rsym value: 0.586 / % possible all: 94.1

-
Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
Cootmodel building
PHASERphasing
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ET9

3et9


Resolution: 1.65→43.29 Å / SU ML: 0.173 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 21.1576
RfactorNum. reflection% reflection
Rfree0.1956 2600 4.94 %
Rwork0.1674 --
obs0.1689 52622 96.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 22.58 Å2
Refinement stepCycle: LAST / Resolution: 1.65→43.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3486 0 39 542 4067
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00683642
X-RAY DIFFRACTIONf_angle_d0.8654978
X-RAY DIFFRACTIONf_chiral_restr0.0581544
X-RAY DIFFRACTIONf_plane_restr0.0055629
X-RAY DIFFRACTIONf_dihedral_angle_d16.10732118
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.65-1.680.29881310.26742555X-RAY DIFFRACTION93.59
1.68-1.710.2861160.2562638X-RAY DIFFRACTION94.48
1.71-1.750.28491320.24142566X-RAY DIFFRACTION94.2
1.75-1.790.25711430.22772615X-RAY DIFFRACTION94.45
1.79-1.830.27231160.21842528X-RAY DIFFRACTION94.26
1.83-1.870.26381460.20622638X-RAY DIFFRACTION95.38
1.87-1.920.23871430.19732581X-RAY DIFFRACTION95.28
1.92-1.980.21491260.182649X-RAY DIFFRACTION95.69
1.98-2.040.20241370.16382598X-RAY DIFFRACTION95.76
2.04-2.120.18671410.16072659X-RAY DIFFRACTION96.62
2.12-2.20.18851260.16052647X-RAY DIFFRACTION96.65
2.2-2.30.23951390.16952627X-RAY DIFFRACTION96.98
2.3-2.420.22581470.17072670X-RAY DIFFRACTION97.24
2.42-2.570.20941440.17122652X-RAY DIFFRACTION97.46
2.57-2.770.17251370.16772684X-RAY DIFFRACTION97.82
2.77-3.050.21141400.16582669X-RAY DIFFRACTION98.11
3.05-3.490.14811460.15042685X-RAY DIFFRACTION98.13
3.49-4.40.15951540.13152685X-RAY DIFFRACTION98.44
4.4-43.30.16751360.15112676X-RAY DIFFRACTION97.57

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more